The invention discloses a nuclear magnetic resonance underground water detection signal noise eliminating method. The method comprises the steps of: recoding response data entry three groups, each of these three sets of data Fourier transform nuclear magnetic resonance to determine the frequency of the data center in each neighborhood contains frequency harmonics, and frequency harmonic structure and the same frequency, and magnetic resonance corresponding data with sine function of the length of the cosine function, and composition and magnetic resonance response data observed signal using independent component analysis for each group observed signals to separate the mixed signal obtained solution for data reconstruction to eliminate frequency harmonic interference, the three groups of removing harmonic frequency data as observational signals, and then use algorithm processing, weaken the remaining random noise. The invention is to eliminate harmonic frequency noise at the same time, the signal will not destroy any details, without laying a reference coil, simple operation, suppress random noise does not require a lot of data, reducing the processing time.